Protein structure networks

Description:

This project is identifying important elements of protein structure by network analysis. We model the protein structure by amino acid or hydrogen-bond networks, where the interaction between the individual elements are obtained from the more detailed X-Ray and NMR structure of the protein. The project is aimed to predict and experimentally verify important amino acids or amino acid groups which play an important role in the biological function of the studied protein. Our target proteins include those of the cytochrome P450 family as key members of drug metabolism.

Publications:

1. Hegedus, T., Gyimesi, G., G�sp�r, E.M., Szalay, K.Z., Gangal, R. and Csermely, P. (2013) Potential application of network descriptions in the conformational changes and protonation states of ABC transporters. Curr. Pharm. Des. 19, 4155-4172, IF: 4.8
   http://arxiv.org/abs/1206.0123
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2. Gáspár, E.M. és Csermely, P. (2012) Rigidity and flexibility of biological networks. Briefings Funct. Genomics 11, 443-456. http://arxiv.org/abs/1204.6389
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3. Szalay-Bekő, M., Palotai, R., Szappanos, B., Kovács, I.A., Papp, B. and Csermely, P. (2012) ModuLand plug-in for Cytoscape: extensively overlapping modules, community centrality and their use in biological networks. Bioinformatics, in press http://arxiv.org/abs/1111.3033
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   The Cytoscape plug-in program and its User Guide can be downloaded from here: http://www.linkgroup.hu/modules.php
4. Csermely, P., Sandhu, K.S., Hazai, E., Hoksza, Z., Kiss, H.J.M., Miozzo, F. Veres, D.V., Piazza, F. and Nussinov, R. (2012) Disordered proteins and network disorder in network representations of protein structure, dynamics and function. Hypotheses and a comprehensive review. Curr. Prot. Pept. Sci. 13, 19-33, IF: 3,9, http://arxiv.org/abs/1101.5865
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5. Csermely, P., Palotai, R. and Nussinov, R. (2010) Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem. Sci. 35, 539-546, IF: 11.6, http://arxiv.org/abs/1005.0348 -- a cover story. Download it!
6. Csermely, P. (2008) Creative elements: network-based predictions of active centres in proteins, cellular and social networks. Trends Biochem. Sci. 33, 569-576, Download it!
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7. Csermely, P. (2008) A network scientists highlights active sites of enzymes, cells, brains and the society. Nature 454, 5 Download it!
   
8. Antal, M.A., Böde, C. and Csermely, P. (2009) Perturbation waves in proteins and protein networks: Applications of percolation and game theories in signaling and drug design. Curr. Prot. Pept. Sci. 10, 161-172, IF: 3.3.
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9. Böde, C., Kovács, I.A., Szalay M., Palotai, R., Korcsmáros, T. and Csermely, P. (2007) Network analysis of protein dynamics. FEBS Lett. 581 (15): 2776-82. IF: 3,5 Download it!